Effect of Rho on transcription of bacterial operons

L factor that is required for beta-galactosidase synthesis is the nusA gene product involved in transcription termination

The DNA-dependent in vitro synthesis of Escherichia coli beta-galactosidase requires the presence of a soluble protein referred to as L factor [Kung, H., Spears, C. & Weissbach, H. (1975) J. Biol. Chem. 250, 1556-1562]. In the present study, comparison of physical, immunological, and biological properties shows that L factor is the product of the E. coli nusA gene. The nusA gene product is known to interact with bacteriophage lambda N gene protein and to prevent premature termination of transcription from the early lambda promoters. Our results suggest that premature transcription termination in the lac operon of E. coli may also be overcome by the nusA protein.

E. coli ribosomal RNA contains sequences homologous to insertion sequences IS1 and IS2

The insertion sequence (IS) elements, IS1 and IS2, present in multiple copies in the Escherichia coli chromosome, are transposable genetic elements of known nucleotide sequence. These elements can modulate gene expression, but it is not known whether they normally function in genetic control. To determine whether IS elements could exert control through specific RNA transcripts, we hybridised lambda NNC1857 r14 (carrying IS1) and pBR322 (carrying a portion of IS2) to Northern blots of E. coli RNA. Regions of homology between the IS elements and ribosomal RNA were observed. Computer analysis of reported nucleotide sequences detected large segments of homology between the IS elements and both 23S and 16S rRNA. Additional homologous sequences in phi X174 and a leader region of a ribosomal protein gene cluster were also detected. The homologous sequence between IS2 and 16S rTNA is the same sequence in phi X174 DNA which codes for the ends of the E and D gene and the start of J. The partial IS sequences may represent silent evolutionary remnants or they could modulate the expression of genes carrying these sequences.

A comprehensive molecular map of bacteriophage lambda

Physical and genetic mapping of deletion mutations has been correlated with the available molecular sizes of the lambda gene products and the DNA base sequence to construct a comprehensive molecular map of the phage lambda genome. The physical length of the DNA making up the left arm from the cos site through gene J is not sufficient to account in a nonoverlapping manner for all the proteins of the sizes reported to be coded, especially in the Nu1--C region. In the right arm all the coding capacity has not been accounted for, and it appears to be oversaturated only in the gam-ral region. The positions of several IS and Tn elements, and of restriction endonuclease cleavage sites are specified.

IS2-43 and IS2-44: new alleles of the insertion sequence IS2 which have promoter activity

The sequence of two new IS2 alleles with promoter activity (IS2-43 and IS2-44) is reported. The alleles are identical and are formed by a 17 bp tandem duplication in an AT-rich region of IS2. This created a new RNA polymerase binding site. A mutation was found that increased the frequency of formation of these 17 bp duplications but not of another class of duplications, the "mini-insertions". This suggested that the mechanisms of formation of the two classes of duplications are different.

Relief of polarity in E. coli depleted of 30S ribosomal subunits

Escherichia coli was depleted of ribosomes by a thermal shock at 47 degrees C which quantitatively destroyed the 30S ribosomal subunits. During recovery in minimal medium at 30 degrees C RNA is synthesized while protein synthesis resumes only after about 90 min. It is shown that lac mRNA is synthesized in the complete absence of ribosomal activity and hence RNA synthesis is not coupled to protein synthesis. Lac mRNA from a series of lac nonsense mutants was examined in both heated and untreated cells. It was found that the polar effect of nonsense mutation is relieved in the absence of ribosomes and that this relief is due to the synthesis of larger mRNA molecules. Since Rho remained active in thermally treated cells, premature termination at secondary signals within the lac operon must also depend on the presence of active ribosomes.

Suppression of polar effects of nonsense mutations by ultraviolet irradiation

Nonsense mutations in capsid genes F and G of phages S13 and phi X174 decreased the expression of genes downstream. These polar effects were suppressed by ultraviolet irradiation of the host before infection. Activities of the downstream genes were restored to between 30 and 95% of their normal levels, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the viral proteins. The effect of ultraviolet irradiation may be to suppress rhodependent termination of transcription. The polarity of one mutation was poorly suppressed by ultraviolet irradiation.

Regional replication of the bacterial chromosome induced by derepression of prophage lambda. III. Role of the replication in escape synthesis of gal operon

Recent evidence suggests that the escape synthesis of gal operon following derepression of the prophage lambda in Escherichia coli K12 involves transcription originating at the lambda promoter (PL) to extend through gal under the conditions in which lambda DNA replication is prevented. Whether the observed expression of gal is due to transcription initiating at PL or at the bacterial promoter for gal (Pgal) was examined in the case of lambda DNA replication being normal. The experiments are based on that two types of transcription are distinguished from each other by the following properties: 1. Pgal-promoted transcription is inhibited by chloramphenicol, while PL-promoted transcription is not. 2. PL-promoted transcription suppresses the polar effect caused by nonsense mutation in a bacterial gene, while Pgal-promoted transcription does not do so. -he results have suggested that gal escape synthesis in lambda-induced lysogen results from transcription which initiates not only at PL but also at Pgal. The Pgal-promoted transcription may be a consequence, direct or indirect, of the concomitant replication of gal DNA.

PL-promoted transcription of the promoter-proximal N-trp region is insensitive to chloramphenicol in the absence of N function

When the trp operon is translocated into the early region of lambda phage, transcription originated at the PL promotor is known to be modified by function of the N gene product so that transcription of the operon continues when translation is blocked by nonsense mutations or by ribosomal antibiotics. When N function is deficient in a phage that joins the trp operon to a point distal to the N gene, deleting the tL site, nonsense mutations (Franklin, 1974) or chloramphenicol (Nakamura et al., accompanying paper) again block transcription of the bacterial operon. However, here we report that transcription over about the first 800 nucleotide pairs starting from the PL promotor of the N-trp operon is still insensitive to chloramphenicol even in the absence of N function. The region covers the full N gene and the initial bit of the trp operon.

Identification of the gal3 insertion in Escherichia coli AS IS2

The gal3 mutation in Escherichia coli, located in the operator-promoter region of the gal operon, is identified as an IS2 insertion in the polar orientation I relative to the direction of transcription. This mutation, which may be considered the earliest example of a polar mutation caused by an IS insertion, is shown by heteroduplex analysis of phage lambdagal3 to be located about 170 base pairs from the promoter-proximal end of the chlD-pgl deletion in lambdagal8. It appears indistinguishable in position, sequence and orientation from the IS2 insertion carried by lambdagal8-490. The endpoints of the bacterial DNA segments in lambdagal3 and lambdagal8 are physically mapped in relation to attL.

Transposable genetic elements as agents of gene instability and chromosomal rearrangements

Transposable genetic elements in prokaryotes and eukaryotes, when inserted at a given locus, can control expression of the locus and cause large scale rearrangements of adjacent DNA sequences. Striking similarities in genetic behaviour between the two groups of elements have led to the proposal of a molecular model of eukaryotic controlling elements, and to suggestions about the part such elements may play in evolution and differentiation.

Suppression of polarity of insertion mutations within the gal operon of E. coli

Phenotypic revertants of galOP::IS1 and galOP::IS2 mutations have been isolated after mutagenesis with nitrosoguanidine, they are probably caused by mutations in gene suA. The polarity suppressor mutations described in this study and a known mutation in gene suA isolated by D. Morse (Morse and Guertin, 1972) suppress polarity caused by IS1 more effectively than that caused by IS2 or IS4. Furthermore, suppressibility is influenced by the site and orientation of IS integration. The synthesis of the three enzymes in galOP::IS suA double mutants is constitutive and the ratio of the three enzymes is altered in comparison to the wild type. The reasons for constitutive synthesis of the galactose enzymes and for the altered ratio of enzyme synthesis are discussed.

Isolation and properties of an inhibitor of Escherichia coli RNA polymerase

An inhibitor of the Escherichia coli RNA polymerase has been isolated from E. coli and has been partially characterized. The inhibitor, a polypeptide of molecular weight 70000, acts to shut off RNA synthesis at about the time that the first round of RNA synthesis is over, preventing any further RNA synthesis. The inhibitor apparently does not recognize specific termination sequences in the DNA template, since it works equally well with double-stranded DNA, single-stranded DNA and poly[d(A-T)] as templates for RNA synthesis, and because the RNA molecules synthesized from T7 DNA appear to be terminated at the same site either in the presence or absence of the inhibitor. Several experiments indirectly indicate that the inhibitor may reversibly bind to the RNA polymerase at the termination step, in a ratio of approximately one inhibitor molecule per polymerase molecule.

Specificity of polarity suppression in E. coli: correction of defects in gene N, but not in gene Q, of phage lambda

The bacterial mutation psuA1, known as (suA) a polarity suppressor, partially relieves all N defects in bacteriophage lambda growth. No evidence is found that psuA1 relieves Q defects in lambda growth. Specific mechanisms of action by the N and Q gene products are discussed. The psuA1 mutation was also found to suppress IS1 type but not IS2 type insertion mutations in lambda.

Isolation and characterization of phi80dgal transducing phages that carry gal operator-promoter insertion mutations

phi80dgal transducing bacteriophages have been isolated by the F-fusion technique of Press et al. (1971) and gal-operator-promoter insertion mutations have been introduced by homogenate formation. Five different phi80dgal isolates have been studied in more detail. One of the phi80 phages transduces the gal operon and gene aroG as well as at least part of the trp-operon; the gal operon of another phi80dgal transducing phage is inverted with respect to the phi80dgal sequences. Heteroduplex DNA mapping indicates that one of the phi80dgal isolates in addition to the gal operon and a portion of the adjacent chromosomal region carries an IS2-element which is derived from the F'gal episome. The isolated phi80dgal phages may be utilized for preparing pure gal mRNA and insertion-RNA as well as pure gal operon DNA.

Efficient suppression of the requirement for N function of bacteriophage lambda by a Rho-defective E.coli suA mutant

The E. coli suA mutant (T82), which is a suppressor of polarity by virtue of its impaired transcription termination factor (rho) activity, is shown to be an efficient suppressor of lambdaN- mutants. The relief of the N requirement by this host is reflected in a substantial restoration of growth and N-dependent beta-galactosidase expression as well as in a partial relief of polarity of N-defective phages.

Regulation of transcription factor rho and the alpha subunit of RNA polymerase in Escherichia coli B/r

Transcriptional termination factor rho, the alpha subunit of RNA polymerase (RNA nucleotidyltransferase nucleosidetriphosphate: RNA nucleotidyltransferase, EC 2.7.7.6), and ribosomal protein S6 were resolved from whole-cell extracts of E. coli B/r by a high-resolution, two-dimensional polyacrylamide gel electrophoretic technique, and were identified through coelectrophoresis with the purified proteins. The regulation of rho, alpha, and S6 was studied, in steady-state cultures of E. coli B/r growing at rates ranging from 0.6 to 2.1 generations per hr, through the use of this gel technique and a double radioisotope labeling procedure. The regulatory patterns of rho and alpha are distinct from, but similar to, one another. Neither rho nor alpha shows the sharply increasing levels with increasing growth rate shown by the ribosomal proteins was exemplified by S6. The difference between the levels of rho and alpha, on the one hand, and S6, on the other, is most pronounced during rapid growth. The regulatory pattern of alpha is interesting, given the recent suggestion that the gene coding for alpha is contranscribed with genes coding for ribosomal proteins.

Suppression of polarity of insertion mutations in the gal operon and N mutations in bacteriophage lambda

Bacterial mutations (psuA and psu) known for their ability to suppress the polarity on nonsense mutations are shown to suppress the polarity of certain insertion mutations in the gal operon. The short insertion, IS1 (800 nucleotide pairs), is about 15 to 50% suppressed, whereas longer insertions, IS2 (1,400 nucleotide pairs), and IS3 (1,200 nucleotide pairs), are not. Some of the polarity suppressor mutations (psu-1, psu-2, and psu-3) are at least partially permissive for N-gene mutations (N7 and N53) of bacteriophage lambda, suggesting a relationship between natural and mutational polar signals. That this relationship may be complex is indicated by the fact that other suppressor mutations, effective in suppressing nonsense or insertion polarity, fail entirely to permit the growth of lambda N mutants.

Naturally occurring sites within the Shigella dysenteriae tryptophan operon severely limit tryptophan biosynthesis

We investigated the structural, functional, and regulatory properties of the Shigella dysenteriae tryptophan (trp.) operon in transduction hybrids in which the cysB-trp-region of Escherichia coli is replaced by the corresponding region from S. dysenteriae. Tryptophan biosynthesis was largely blocked in the hybrids, although the order of the structural genes was identical with that of E. coli. Nutritional tests and enzyme assays revealed that the hybrids produced a defective anthranilate synthetase (ASase). Deletion mapping identified two distinct sites in trpE, each of which was partially responsible for the instability and low activity of ASase. We also discovered a pleiotropic site trpP (S) that maps outside the structural gene region and is closely linked to the S. dysenteriae trp operator. trpP (S) reduced the rate of trp messenger ribonucleic acid synthesis, and consequently trp enzyme levels, 10-fold relative to wild-type E. coli. In recombinants in which the structural genes of E coli were under the control of the S. dysenteriae promoter, enzyme levels were also reduced 10-fold. In some fast-growing revertants of the original hybrids, the rates of trp messenger ribonucleic acid synthesis and levels of tryptophan synthetase were restored to values characteristic of wild-type E.coli. Thus, the Trp auxotrophy associated with the S dysenteriae trp operon derives from the combination of a defective ASase and decreased expression of the entire operon imposed by trpP (S).

Stimulation in trans of synthesis of E. coli gal operon enzymes by lambdoid phages during low catabolite repression

The infection of E. coli cells with different lambdoïd prophages triggers a stimulation of galactokinase synthesis when cells are grown in a medium giving rise to a mild catabolite repression (tryptone broth) with an inducer of the gal operon (fucose). These results show that during phage infection (or induction) some factor acting in trans is produced which is able to overcome efficiently catabolite repression of the kinase cistron. Using different strains of lambdapbio252 (pam, qam, "hl), lambdapbio256Hl and lambdaNNS7 we have concluded that the factor is the N gene product which is known for its anti- p(rho) action. Studies of the whole gal operon in the same conditions show that epimerase unlike transferase and galactokinase is practically insensitive to catabolite repression by tryptone broth and that viral development has a low effect on it. This indicates that there is an internal modulation of gal operon expression. A mRNA termination site sensitive to the p factor is known in the gal operon between galE and galT. Another site weaker than this one might exist between galE and operator-promoter region.

Effects of bacteriophage T4-induced modification of Escherichia coli RNA polymerase on gene expression in vitro

After T4 bacteriophage infection of E. coli a complex series of events take place in the bacterium, including gross inhibition of host transcription and discrete changes in the classes of the genes of T4 that are transcribed. Accompanying these changes in the pattern of transcription one finds T4-induced changes in the RNA polymerase (EC 2.7.7.6; nucleosidetriphosphate:RNA nucleotidyltransferase). The effects of modified polymerase on transcription can be advantageously analyzed in a DNA-directed cell-free system for protein synthesis. In this system gene activity is measured indirectly by the amounts and types of proteins sythesized. In the DNA-directed cell-free system this modified polymerase, like normal polymerase, transcribes T4 DNA with a high efficiency but transcribes bacteriophage lambda and host DNA very poorly. Polymerase reconstruction experiments show that modification of the alpha subunit of the RNA polymerase is sufficient for inhibition of host transcription. Host transcription is also inhibited in vitro by T4 DNA. This latter type of inhibition is presumed to involve competition between host DNA and T4 DNA for some factor essential for transcription. The T4-modified polymerase transcribes from T4 DNA many of the same genes as normal unmodified polymerase; it also shows a capability for transcribing certain "non-early" T4 genes which is enhanced in the presence of protein-containing extracts from T4-infected cells.

The nature of the gal3 mutation of Escherichia coli

The gal3 mutation of the galactose operon of E. coli, first described by Morse, Lederberg, and Lederberg in 1956, exhibits several unique and unusual properties. This mutation originated spontaneously and also reverts spontaneously, but fails to respond to various chemical mutagens. It is extremely polar, but the polarity is not relieved by nonsense suppressors. The gal+ revertants are of at least two different kinds. One class of revertants is stable and exhibits inducible enzyme synthesis, whereas the other class is unstable and constitutive. The properties of gal3 can be explained by the assumption that this mutation was caused by the insertion of a DNA sequence in the operator-promoter region of the gal operon. This proposal was tested by the construction of a gal3 derivative of a lambdagal+ phage and comparison of the physical properties of the two phages. Density-gradient centrifugation studies indicated that the gal3 mutation was accompanied by a 0.0033 g/ml increase in the buoyant density of the phage. This increase in density corresponds to the addition of 1200 base pairs. This observation was confirmed by electron microscopy of lambdagal+/lambdagal3 heteroduplexes. A single-stranded addition loop, 1160 base pairs in length, was found at a fixed position. It was concluded that the gal3 mutation was caused by the insertion of a sequence similar to IS3 in length. These studies also permit an estimation of the physical size of the gal operon. It is found to be 3600 base pairs long, separated from the attlambda (B.P') site by approximately 14000 base pairs.

Transcription termination factor rho activity is altered in Escherichia coli with suA gene mutations

Rho factor has been purified from a strain of E. coli containing the Su78 mutation in the suA gene and assayed in another strain with an amber mutation in the suA gene. The rho from the Su78 mutant strain is present in normal amounts but has altered termination function; it does not terminate transcription at some sites that are recognized effectively by the rho factor from the isogenic wild-type strain. Rho in cells with an amber mutation in the suA gene has been assayed by its RNA-dependent ATPase activity. Extracts of cells of this strain have only 9% as much of this rho activity as extracts of cells of the isogenic wild-type strain. These results suggest that rho is the product of the suA gene. Since mutations in the suA gene are known to decrease polar effects of mutations in other genes, it is also suggested that rho factor is at least partially responsible for polar effects.

Regulation of galactose operon at the gal operator-promoter region in Escherichia coli K-12

The capR (lon) product controls expression of the gal operon independently of the galR repressor. Previously, mutations of the gal operon have been isolated that are semiconstitutive and alter response to the capR and/or capT product. Such mutants imply the existence of a distinct site in the operon that responds to capR (capT) control. This mutation could be either in a site near the operator-distal end of the galE gene, which signals rho factor termination of transcription in vitro or in a site in the operator-promoter region. Bacteriophage U3 was used to isolate galE mutations in HC2142 (a mutant exhibiting reduced response to capR control). P1 transduction was used to cross these mutants with a set of galE gene deletion. Analysis of the resulting Gal+ recombinants indicates that the regulatory site is in the operator-promoter region. Hence, it is unlikely that capR functions in control as an anti-rho factor at the operator-distal end of the galE gene, but more likely as previously suggested, at a second operator distinct from one responding to galR repressor control. Upon induction with D-fucose, a promoter mutant (UV211) isolated previously expressed 20 to 30% of the galactose enzymes that the wild type exhibited in the presence of the inducer D-fucose. The effects of various mutations in cya, capR, and galR on galactokinase synthesis in this mutant were determined. Galactokinase was derepressed by capR as well as galR, but the presence or absence of the cya gene product was unimportant.

Release of polarity in Escherichia coli by gene N of phage lambda: termination and antitermination of transcription

The induction of lambda prophage provokes the constitutive expression of the adjacent gal operon in E. coli. This "escape synthesis" can result from transcription that initiates at a phage promoter and extends into the gal operon. The effect requires the product of the lambda gene N. N-mediated transcription not only fails to terminate at the prophage-bacterial junction and at the ends of bacterial operons, but ignores termination signals caused by polar insertions or ochre mutations within gal. Suppression of polarity by N-function is a cis-effect; only transcription initiated at the phage promoter is influenced. We propose that the transcription complex is influenced by N-product to become termination-resistant at a site in the phage genome (juggernaut model). This site appears to be at or near the phage promoter.

An RNA-dependent nucleoside triphosphate phosphohydrolase (ATPase) associated with rho termination factor

Highly purified rho termination factor from Escherichia coli catalyzes an RNA-dependent hydrolysis of ribonucleoside triphosphates to nucleoside diphosphates and inorganic phosphate. In the presence of poly(C), a specific activity of 100 mumole of ATP hydrolyzed per min/mg has been measured. The phosphohydrolase activity appears to be associated with the protein responsible for termination of RNA synthesis, but a functional relationship between the two activities is not yet evident. Hydrolysis of nucleoside triphosphates occurs in the absence of termination and without any extensive degradation of RNA.

Multiple regulation of the galactose operon-genetic evidence for a distinct site in the galactose operon that responds to capR gene regulation in Escherichia coli K-12

Previous results demonstrated that the capR (lon) locus, which is not linked to the gal operon, independently controls the synthesis of the gal operon enzymes and gal mRNA, i.e., galO(+)capR9 strains are derepressed 4- to 6-fold as compared to galO(+)capR(+) strains. A mutation has been isolated and localized in the galactose operator region that defines a new and distinct site of control. Mutation in this site, designated galO(capR+), causes a 4-fold increase in the galactose enzymes, galactokinase (EC 2.7.1.6) and UDP-galactose-4-epimerase (EC 5.1.3.2), in a capR(+) background. These mutants exhibit a reduced response to regulation by the unlinked regulator gene capR (lon). However, the galO(capR+) mutants are still subject to control by the galR repressor, since they can be further derepressed by growth in the presence of D-fucose. They also synthesize more galactokinase when grown in glycerol as compared to glucose. Thus there are now at least three, and probably four, sites for control of mRNA synthesis in the operator-promoter regions of the gal operon, making it one of the most complex control systems to date for a single operon in bacteria. The complexity is sufficient to accommodate models for differentiation in higher organisms that require more than one "switch" to control a single group of genes.